Cellular editing of RNA can lead to the recoding of expressed sequences before they mature to their functional gene products, such as proteins or regulatory RNAs, and represents a hidden layer of genetic information and regulation. Often, the recoding events are essential for the normal function of the gene product (for example creating an open reading frame), in other cases RNA editing creates additional variation and phenotypic diversity since both the edited and the non-edited versions of the product are functional and co-exist. It is necessary to understand the mechanisms of RNA editing in order to elucidate the overall physiological impact of this phenomenon.

This major new work presents an up-to-date overview of RNA editing. All the chapters here have been written by experts in the various research areas and describe key recent findings as well as exploring current frontiers in the mechanisms and functional roles of RNA editing. The chapters span the editing of protein coding mRNAs, small regulatory RNAs, tRNAs and non-coding sequences. Also included are studies employing bioinformatics to identify and predict RNA editing sites as well as the evolution of RNA modification.

An essential text for anyone interested in RNA editing and modification, RNA structure and function, post-transcriptional regulation, and the regulation of gene expression and a recommended purchase for molecular biology libraries.

Reviews

"an up-to-date overview of the field ... will be useful to students as well as experienced researchers ... an essential book for anyone interested in RNA editing and modification, RNA structure and function, post-transcriptional regulation, and the regulation of gene expression. There are not many books available on this subject."fromDoodys

A large proportion of the recoding events mediated by RNA editing are in mRNAs that encode ion channels and transporters. The effects of these events on protein function have only been characterized in a few cases. In even fewer instances are the mechanistic underpinnings of these effects understood. This chapter focuses on how RNA editing affects protein function and higher order physiology. In mammals, particular attention is given to the GluA2, an ionotropic glutamate receptor subunit, and Kv1.1, a voltage-dependent K+ channel, because they are particularly well understood. In addition, work on cephalopod K+ channels and Na+/K+ ATPases has also provided important clues on the rules used by RNA editing to regulate excitability. Finally, we discuss some of the emerging targets for editing and how this process may be used to regulate nervous function in response to a variable environment.

2. Mechanisms and Functions of RNA Editing in Physarum polycephalum

Jonatha M. Gott

Mitochondrial RNAs in the acellular slime mold Physarum polycephalum are subject to the widest range of editing events observed thus far. Mitochondrial RNAs differ from the mitochondrial genome at over 1300 sites, and both coding (mRNAs) and non-coding RNAs (rRNAs and tRNAs) are affected. At least three distinct editing mechanisms are needed to account for the different forms of editing observed in the mitochondrial transcriptome: nucleotide insertions and deletions, C to U changes, and specific alterations at the 5' end of tRNAs. Nucleotide insertions are co-transcriptional and require flanking regions of the template, but the exact signals that specify the site of nucleotide insertion and the identity of the nucleotide to be added remain an enigma. The rare instances of base changes and replacement of the first nucleotide of mitochondrial tRNAs are not directly linked to transcription and are likely to occur via processes related to those previously described in other mitochondrial editing systems.

3. tRNA Modification and Editing

Bhalchandra S. Rao and Jane E. Jackman

Transfer RNAs (tRNAs) are critical players in gene expression due to their essential function as adaptor molecules. Yet, the true enigma in their biological function lies in their ability to consistently transport 22 distinct amino acids, as specified by their identity, to the decoding center with extraordinarily high fidelity, yielding functional polypeptides. Previous research has indicated that mechanisms underlying the establishment of tRNA identity and high fidelity aminoacylation are tightly linked to recognition of an optimal three dimensional structure of tRNAs. Hence it is not surprising that diverse biochemical pathways of tRNA processing have evolved in all three domains of life that directly influence the functionality and structural integrity of tRNAs. The following chapter reviews tRNA modification and editing mechanisms that directly influence tRNA homeostasis in all three domains of life.

4. Coordination of RNA Editing with Other RNA Processes in Kinetoplastid Mitochondria

Jorge Cruz-Reyes and Laurie K. Read

The extraordinary RNA editing by U insertion and U deletion in mitochondrial mRNAs is arguably the best characterized process in kinetoplastids. However, much less is known about ancilliary factors of the editing multiprotein enzyme core. This enzyme architecture and basic catalysis guided by small non-coding gRNAs have enjoyed central stage, compared to other aspects in the biology of editing substrates, from biogenesis to translation. Many mRNAs and thousands of gRNAs are undoubtedly targeted by numerous factors that regulate unwinding, annealing, stability, assembly into editing enzymes, and translation. Recent years have seen a virtual explosion in the discovery of editing accessory factors. This chapter discusses the progress in this area, and frames a working model whereby the editing machinery is functionally and physically linked to pre and post editing events through a dynamic higher-order network of protein and RNA interactions.

We review the progress in the past decade in structural studies of the proteins and RNAs associated with the U-insertion/deletion RNA editing (or k-RNA editing) in the mitochondrion of trypanosomes. This review includes the electron microscopy studies of RNA editing complexes. Beyond the intellectual quest to understand the structural basis of RNA editing, these studies share the goal of using structures of essential proteins to design better inhibitors of RNA editing for medical and research purposes.

6. RNA Editing and Small Regulatory RNAs

Bjorn-Erik Wulff and Kazuko Nishikura

Adenosine-to-inosine (A-to-I) editing of double-stranded RNA (dsRNA) is catalyzed by members of the adenosine deaminase acting on RNA (ADAR) family, which is conserved from man to sea anemone. It has recently become clear that the most common substrates of ADARs are non-coding RNAs, including small regulatory RNAs like microRNAs (miRNAs), short interfering RNAs (siRNAs) and endogenous siRNAs (esiRNAs). These mediate post-transcriptional gene silencing (PTGS) by base pairing to complementary transcripts. This review discusses the effects ADARs exert on small regulatory RNA pathways and the resulting biological consequences. This discussion includes how ADAR substrate specificity is controlled, how ADARs both edit and sequester substrates, how ADARs affect the miRNA pathway by editing miRNA targets and efforts to discover novel edited adenosines affecting small regulatory RNA pathways.

7. Deaminase-Dependent and Deaminase-Independent Functions of APOBEC1 and APOBEC1 Complementation Factor in the Context of the APOBEC Family

Harold C. Smith

Two decades of research revealed the mechanism for site-specific, apolipoprotein B (apoB) mRNA C to U editing and its developmental and metabolic regulation. The field began to lose momentum while many open questions remained. This was due to perceived impasses in translational research endpoints: (1) liver is the most significant organ in the metabolism of cholesterol- and triglyceride-rich lipoproteins and despite active and regulated hepatic editing in rodent models, human liver does not express the cytidine deaminase APOBEC1 required for apoB mRNA editing. (2) Mammals express APOBEC1 in their small intestines where 100% of the apoB mRNA is edited in adults but this activity is constitutive. (3) Expression of APOBEC1 is not essential for life in mice. In the past few years there has been a resurgence in interest because: (1) APOBEC1 edits the 3' UTRs of multiple mRNAs and either alone or together with its RNA-binding cofactor, A1CF, may regulate mRNA stability and translation in diverse tissues. (2) A1CF is required for embryological development, acting through a mechanism that may be unrelated to APOBEC1. (3) Discovery of dC to dU DNA mutational activity by APOBEC1 raises new questions of its oncogenic potential. This review will consider past and current discoveries relative to the exciting new research opportunities in the field.

8. Identification of RNA Editing Sites: a Survey of the Past, Present, and Future

Meng How Tan and Jin Billy Li

RNA editing is a post-transcriptional mechanism whereby genomically encoded information is altered at the level of the transcript. We describe in this chapter how RNA editing sites can be identified. The pace of discovery in the past few decades was dependent on the sequencing technologies available at a particular time. At the beginning when DNA sequencing had just been developed and automated, the identification of RNA editing sites was slow and often occurred by chance. Over time, as more and more sequences were deposited in databases, it became possible for scientists to computationally mine the databases for more editing sites. In recent years, with the development of ultra-high throughput sequencing technologies whereby millions to billions of DNA molecules are sequenced simultaneously, scientists can now uncover RNA editing sites in a genome-wide manner. However, extra care has to be taken during the analysis process to remove artifacts and to ensure that true editing sites are identified.

9. Regulation of Gene Expression Through Inosine-containing UTRs

Heather Hundley

Adenosine deaminases that act on RNA (ADARs) "edit" RNA by converting adenosines to inosines within double-stranded regions. Because adenosine and inosine have different base-pairing properties, editing alters RNA structure. Furthermore, as inosine is recognized as guanosine by the translation and splicing machinery, editing can alter the protein coding potential and splicing patterns of mRNA. In fact, the ability to diversify the proteome is an important function of ADARs. However, it is now clear that editing within coding regions is rare compared to editing of noncoding regions, such as introns and untranslated regions (UTRs). Although editing of UTRs is widespread, the function of these modifications is unclear. Here, we review the diverse fates that have been reported for inosine-containing RNAs and specifically discuss whether editing is required for these outcomes.

10. ADARs and the Viral Life Cycle

Sara Tomaselli, Federica Galeano, Franco Locatelli and Angela Gallo

All viruses that have dsRNA structures at any stages of their life cycle may potentially undergo RNA editing mediated by ADAR enzymes. Indeed, a number of reports describe A-to-I sequence changes in viral genomes and/or transcripts that are consistent with ADAR activity. These modifications can appear as either hyperediting during persistent viral infections or specific RNA editing events in viral dsRNAs. It is now well established that ADAR enzymes can affect virus interaction with their host in both an editing-dependent and -independent manner, with ADARs playing for both sides: the host and the virus. Despite the discovery of editing events on viral RNA dates back to thirty years ago, the biological consequences of A-to-I changes during viral infection is still far to be completely elucidated. In particular, the proviral role played by ADAR1, partly due to PKR inhibition, together with its antiviral effect following hyperediting events, put in evidence the complex role played by RNA editing in the regulation of viral infections and innate immune response.